Role of Epigenetic Changes in the Etiology of Human Diseases
The field of epigenetics is ever-growing and considered to be a relatively new branch of genetic research. However, the concept dates back to the 1940s when it was understood as a mechanism that involved gene and gene-product interactions responsible for phenotypic expression1. Epigenetics is now understood as stable, heritable changes in gene expression that are not associated with changes in the actual DNA sequence. That means that the phenotype can change without changing the actual genotype. There are a number of means by which gene expression is regulated. One of the most extensively studied epigenetic mechanisms is DNA methylation. The presence or absence of a methyl group on strategic locations of a gene determines how, if, or when that gene will be expressed. Alterations in the patterns of DNA methylation have been well-studied and known to be associated with the development of disease states or developmental defects. Changes in DNA patterns can occur via a demethylation and hypermethylation. Other mechanisms include histone modification (biochemical alterations of proteins that package DNA) and microRNA regulation2, 3.
Normal embryonic development is also dependent upon properly functioning epigenetic mechanisms. Temporal and structural alterations in DNA methylation patterns lead to a number of developmental defects in animals and humans. When speaking of temporal alterations, a DNA methylation pattern that is appropriate at one stage or point in time of development may not be appropriate for another. Further, an alteration in a specific anatomical region may not occur in another, or even if it does, may not lead to an adverse change. For example, a study by Branch and Henry demonstrates that altered gene expression in mice is associated with 5-aza-2′-deoxycytidine-induced (DNA demethylating agent) changes in Hox gene expression leading to limb defects4. The particular effect was specific for hindlimbs and only during mid-gestation.
It was not previously thought that xenobiotic-induced gene expression changes not associated with DNA sequence modification could be inherited. Cisneros and Branch demonstrated that a toxicant exposure can lead to defects in subsequent generations of mice that were not themselves exposed to the toxicant5. The defects were shown to be associated with epigenetic changes instead of mutations in actual DNA sequences. The science of epigenetic inheritance is now widely studied in regard to observations seen throughout generations in humans.
A number of developmental abnormalities in humans have been linked to epigenetic alterations. Beckwith-Weidman Syndrome (BWS) is a developmental disease characterized as an outgrowth disorder and associated with a predisposition towards tumor development. Dysregulation of imprinting has been linked to this developmental disorder. Imprinting refers to the expression of genes based on their origin from one parent. In other words, if an allele that is inherited from the mother is imprinted (marked epigenetically), it will not be expressed, but the one from the father will be. In BWS, epigenetic alterations are associated with the dysregulation of specific imprinted genes on chromosome 11p15.56. Beckwith-Weidman syndrome and other imprinting disorders have been associated with assisted reproductive technologies, with epigenetic alterations as an important contributor to this phenomenon.
Congenital heart defects (CHD) have been linked to altered DNA methylation. Chowdhury et al.7 determined the methylation status of thousands of GpG sites from white blood cell DNA taken from pregnant women (CHD-affected and unaffected pregnancies). Results of the study indicate that altered maternal DNA methylation may be associated with CHDs. Changes in the maternal epigenetic status may be due to a number of factors including environmental, metabolic, and genetic. Alterations in maternal methylation may directly affect the developing embryo or fetus or even make the conceptus more susceptible to toxic agents.
Epigenetics in Diagnostics
Epigenetic biomarkers are valuable targets for accurate diagnoses of a number of diseases. Methods to determine differential DNA methylation to distinguish or detect rare diseases have been and still are being developed. DNA methylation detection methods are studied as a means to analyze blood or fecal specimens as a non-invasive diagnostic approach for colorectal cancer (CRC). Coppedè et al. found that methylation analysis of septin 9 and vimentin genes are viable candidates for the non-invasive diagnosis of CRC8. In the case of ovarian cancer, studies by McCluskey et al. showed that the difference in p16 gene methylation allow distinguishing between benign and malignant ovarian tumors9.
Epigenetic analysis can also facilitate the diagnosis of diseases other than cancer. Facioscapulohumeral muscular dystrophy (FSHD) 1 can be diagnosed by using DNA restriction methods, electrophoresis, and southern blot; however, FSHD2 cannot be diagnosed by this means. Jones et al. determined that FSHD1 and FSHD2 can be diagnosed and distinguished by investigating the epigenetic signature of genomic DNA isolated from blood or saliva10. The analysis of epigenetic markers is also being developed and shows promise as a diagnostic tool for Alzheimer´s disease. Epigenetic alterations have been identified in relation to Alzheimer´s disease–related biochemical pathways. This information has the utility to determine epigenetic markers for use in the diagnosis of Alzheimer´s disease11.
The ability to perform prenatal testing for developmental defects using epigenetic markers is being developed and has a very promising future. Using chorionic villus samples from women with healthy pregnancies, Paganini et al. tested the methylation levels of various imprinted loci associated with BWS12. They were able to determine that the ICR1 and ICR2 loci could be reliable targets to diagnose BWS by testing methylation status of these loci. Noninvasive diagnosis of Down´s Syndrome via next-generation sequencing (NGS) using maternal blood is already possible for the detection of trisomy on chromosome 2113. Also, the use of methylated DNA immunoprecipitation combined with real-time quantitative PCR can be performed noninvasively. With this approach, Papageorgiou et al. achieved noninvasive prenatal detection of trisomy 21 using maternal peripheral blood14.
Marketable epigenetic-based therapies are currently being investigated. Potential targets for these therapies include DNA methylation and histone acetylation inhibitors15. However, there is already a drug, 5-azacytine (a DNA demethylating agent), which has helped open the door to the study and characterization of DNA methylation control of gene expression. This drug is used as a treatment for myeloid leukemia and myelodysplastic syndromes.
Future Human Clinical or Epidemiological Studies
Not only do changes or exposures occurring in the mother affect fetal outcome, but those that occur in the father may also lead to developmental abnormalities in offspring. Mouse studies showed that paternal feeding of diets deficient in vitamin B9 or folate led to higher developmental defects in offspring when compared to healthy paternal feeding16. In the sperm of the male mice fed folate-deficient diets, epigenetic markers were altered in genes associated with cancer, schizophrenia, and other conditions and diseases. Investigating this via human clinical or epidemiological studies is paramount and would prove most interesting.
There are state-of-the art technologies available to study epigenetic status in biological tissues. Next-generation sequencing and microarray approaches can be used to detect changes in DNA methylation patterns. The combination of bisulfate conversion with NGS has permitted the genome-wide analysis of DNA methylation17. In addition, detecting DNA methylation differences between tissue types has been accomplished with microarray technology18. These technologies have allowed the discovery of connections between altered epigenetic mechanisms and disease. Not only has this allowed an increase in the understanding of disease etiology, but may reveal therapeutic targets to restore normal physiological function.
1) Waddington CH. The epigenotype. 1942. International journal of epidemiology. 2012;41(1):10-3.
2) Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, et al. Relationship between nucleosome positioning and DNA methylation. Nature. 2010;466(7304):388-92.
3) Mattick JS, Makunin IV. Non-coding RNA. Human molecular genetics. 2006;15 Spec No 1:R17-29.
4) Branch S, Henry-Sam G. Altered hox gene expression and cellular pathogenesis of 5-aza-2′-deoxycytidine-induced murine hindlimb dysmorphogenesis. Toxicologic pathology. 2001;29(5):501-6.
5) Cisneros FJ, Branch S. In utero exposure to 5-aza-2’-deoxycytidine induces multigenerational abnormal development: role of the inheritance of altered DNA methylation patterns. Birth Defects Res A Clin Mol Teratol 2005;73(5):293.
6) Weksberg R, Shuman C, Beckwith JB. Beckwith-Wiedemann syndrome. European journal of human genetics. 2010;18(1):8-14.
7) Chowdhury S, Erickson SW, MacLeod SL, Cleves MA, Hu P, Karim MA, et al. Maternal genome-wide DNA methylation patterns and congenital heart defects. PloS one. 2011;6(1):e16506.
8) Coppede F, Lopomo A, Spisni R, Migliore L. Genetic and epigenetic biomarkers for diagnosis, prognosis and treatment of colorectal cancer. World journal of gastroenterology : WJG. 2014;20(4):943-56.
9) McCluskey LL, Chen C, Delgadillo E, Felix JC, Muderspach LI, Dubeau L. Differences in p16 gene methylation and expression in benign and malignant ovarian tumors. Gynecologic oncology. 1999;72(1):87-92.
10) Jones TI, Yan C, Sapp PC, McKenna-Yasek D, Kang PB, Quinn C, et al. Identifying diagnostic DNA methylation profiles for facioscapulohumeral muscular dystrophy in blood and saliva using bisulfite sequencing. Clinical epigenetics. 2014;6(1):23.
11) Adwan L, Zawia NH. Epigenetics: a novel therapeutic approach for the treatment of Alzheimer’s disease. Pharmacology & therapeutics. 2013;139(1):41-50.
12) Paganini L, Carlessi N, Fontana L, Silipigni R, Motta S, Fiori S, et al. Beckwith-Wiedemann syndrome prenatal diagnosis by methylation analysis in chorionic villi. Epigenetics : official journal of the DNA Methylation Society. 2015;10(7):643-9.
13) Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proceedings of the National Academy of Sciences of the United States of America. 2008;105(42):16266-71.
14) Papageorgiou EA, Karagrigoriou A, Tsaliki E, Velissariou V, Carter NP, Patsalis PC. Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21. Nature medicine. 2011;17(4):510-3.
15) Xu Z, Li H, Jin P. Epigenetics-Based Therapeutics for Neurodegenerative Disorders. Current translational geriatrics and experimental gerontology reports. 2012;1(4):229-36.
16) Lambrot R, Xu C, Saint-Phar S, Chountalos G, Cohen T, Paquet M, et al. Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes. Nature communications. 2013;4:2889.
17) Zhang Y, Jeltsch A. The application of next generation sequencing in DNA methylation analysis. Genes. 2010;1(1):85-101.
18) Schumacher A, Kapranov P, Kaminsky Z, Flanagan J, Assadzadeh A, Yau P, et al. Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research. 2006;34(2):528-42.